If you are a clinical lab looking to build or accelerate your NGS testing capability where do you start? The components of success can be overwhelming - planning, assay design, validation, clinical lab workflow, informatics, and interpretation.
During this one-hour webinar, BG Jones, SVP of Business Development for PierianDx, who has 23 years of experience in healthcare IT and genomics technology, will demonstrate how to pull it all together using "Actionable Intelligence" - a combination of machine learning and human expertise to achieve clinically actionable insights.
Rakesh Nagarajan, MD, PhD and founder of PierianDx, discusses the rise of precision medicine programs and makes the business case for healthcare institutions to build their own clinical NGS testing programs.
Is insourcing NGS testing worth it?
Dartmouth-Hitchcock has experienced nearly 40% savings by bringing NGS testing in-house. A recent AMP study using non-small cell lung cancer as an example cites $2.7 million in anticipated savings.
In-house NGS testing is the foundation of any modern precision medicine program. It can have a profound effect on patient care. And, as these examples show, a strong business case can be made.
How have Dartmouth-Hitchcock and other progressive institutions been so successful despite myriad challenges?
Join us for a webinar on May 31st at 12pm ET as Eric Loo, MD (Dartmouth-Hitchcock) and Rakesh Nagarajan, MD, PhD (PierianDx) explore answers to this question and more.
In this webinar you will learn:
How recent precision medicine trends are driving strong market growth for clinical NGS and other complex molecular testing.
How to make a strong business case for in-house NGS testing.
Challenges your institution is likely to face by insourcing.
Blueprints for overcoming these challenges, including reimbursement.
Webinar analyzing complex genomic variants in somatic cancer Lisa Owen
Next generation sequencing (NGS) technologies facilitate the accurate detection of genetic and genomic variants. Yet the process of analyzing and classifying more complex alterations remains challenging.
In this slide deck, which is a companion to the webinar presented on February 21, 2019 and located here (https://www.pieriandx.com/analyzingcomplexgenomicvariants) you’ll learn how to analyze complex genomic alterations, such as gene fusions, splice-site mutations, and co-occurring variants within the context of somatic cancer.
Cancer Diagnostics Reference Laboratory / NeoGenomics April 2014 investors company overview presentation. This presentation highlights the following:
--Fast growing cancer genetics lab servicing Oncologists, Pathologists and Hostpitals
--Strategic client partnerships created by "Tech-Only" model
--Dynamic, rapidly-growing and consolidating industry
Industry-leading revenue & test volume growth
--Strong productivity and operating leverage leading to accelerating cash flow and net income
--Strong Management Team with large cap lab experience
Darby Kammeraad, a Field Application Scientist at Golden Helix, gives some insight into the advantages of VarSeq's capability with annotations. The number of annotation topics to cover is seemingly limitless. In this webcast, he focuses on key elements that demonstrate the value of Golden Helix's curated annotations available in VarSeq and address some important considerations from our users. We also cover the types and effective utilization of annotations in VarSeq. Finally, he covers how users can create their own annotation sources from the Convert Wizard tool.
An Exploration of Clinical Workflows in VarSeqGolden Helix
In this webcast, we feature several example workflows and helpful features in the VarSeq that can be used in the clinic. We discuss options for conducting a comprehensive gene panel analysis for cancer or hereditary diseases. Then we introduce an example of a single exome workflow that goes from an unfiltered VCF created by a secondary analysis pipeline to a report containing information about interesting variants. Finally, we walk through an example of a trio analysis showcasing a variety of different filter options as well as inheritance patterns. All these workflows will result in a customizable clinical report.
Rakesh Nagarajan, MD, PhD and founder of PierianDx, discusses the rise of precision medicine programs and makes the business case for healthcare institutions to build their own clinical NGS testing programs.
Is insourcing NGS testing worth it?
Dartmouth-Hitchcock has experienced nearly 40% savings by bringing NGS testing in-house. A recent AMP study using non-small cell lung cancer as an example cites $2.7 million in anticipated savings.
In-house NGS testing is the foundation of any modern precision medicine program. It can have a profound effect on patient care. And, as these examples show, a strong business case can be made.
How have Dartmouth-Hitchcock and other progressive institutions been so successful despite myriad challenges?
Join us for a webinar on May 31st at 12pm ET as Eric Loo, MD (Dartmouth-Hitchcock) and Rakesh Nagarajan, MD, PhD (PierianDx) explore answers to this question and more.
In this webinar you will learn:
How recent precision medicine trends are driving strong market growth for clinical NGS and other complex molecular testing.
How to make a strong business case for in-house NGS testing.
Challenges your institution is likely to face by insourcing.
Blueprints for overcoming these challenges, including reimbursement.
Webinar analyzing complex genomic variants in somatic cancer Lisa Owen
Next generation sequencing (NGS) technologies facilitate the accurate detection of genetic and genomic variants. Yet the process of analyzing and classifying more complex alterations remains challenging.
In this slide deck, which is a companion to the webinar presented on February 21, 2019 and located here (https://www.pieriandx.com/analyzingcomplexgenomicvariants) you’ll learn how to analyze complex genomic alterations, such as gene fusions, splice-site mutations, and co-occurring variants within the context of somatic cancer.
Cancer Diagnostics Reference Laboratory / NeoGenomics April 2014 investors company overview presentation. This presentation highlights the following:
--Fast growing cancer genetics lab servicing Oncologists, Pathologists and Hostpitals
--Strategic client partnerships created by "Tech-Only" model
--Dynamic, rapidly-growing and consolidating industry
Industry-leading revenue & test volume growth
--Strong productivity and operating leverage leading to accelerating cash flow and net income
--Strong Management Team with large cap lab experience
Darby Kammeraad, a Field Application Scientist at Golden Helix, gives some insight into the advantages of VarSeq's capability with annotations. The number of annotation topics to cover is seemingly limitless. In this webcast, he focuses on key elements that demonstrate the value of Golden Helix's curated annotations available in VarSeq and address some important considerations from our users. We also cover the types and effective utilization of annotations in VarSeq. Finally, he covers how users can create their own annotation sources from the Convert Wizard tool.
An Exploration of Clinical Workflows in VarSeqGolden Helix
In this webcast, we feature several example workflows and helpful features in the VarSeq that can be used in the clinic. We discuss options for conducting a comprehensive gene panel analysis for cancer or hereditary diseases. Then we introduce an example of a single exome workflow that goes from an unfiltered VCF created by a secondary analysis pipeline to a report containing information about interesting variants. Finally, we walk through an example of a trio analysis showcasing a variety of different filter options as well as inheritance patterns. All these workflows will result in a customizable clinical report.
Clinical labs must have the ability to go from a collection of samples and associated variants to a professional report documenting a short list of clinically relevant variants. Cancer Gene Panels are a common clinical application for genetic tests. In this webcast we will show how VarSeq and VSReports can be used to go from an unfiltered variant file created by a secondary analysis pipeline to a report containing information about interesting variants.
This webcast will highlight VarSeq's support for Cancer Gene Panels and Tumor-Normal workflows by demonstrating:
• Variant, Region and Sample Quality Assurance
• Filtering to variants in targeted cancer genes relevant to the tumor type
• Summarizing variants in a clinical report
Introducing VSClinical AMP Guidelines: A Comprehensive Workflow for NGS Testi...Golden Helix
The individualized nature of tumors requires genomic testing for providing the best outcomes for patients. Next-Generation Sequencing enables the detection of small mutations, copy number changes, and common fusions affordably and with high precision. However, the interpretation of these detected variants is arduous without a comprehensive analytical workflow that can incorporate all the bioinformatics and clinical evidence involved in following the AMP guidelines for the scoring and reporting of somatic mutations.
Please join us as we reveal the AMP guidelines workflow support in VSClinical. We will cover the entire post-sequencing analytical workflow from FASTQ to clinical report, including:
- Apply the AMP Tiers to the available clinical evidence for Drug Sensitivity, Drug Response, Prognostics and Diagnostics
Support small mutations (SNPs, InDels) along with CNVs, fusions and wild-types as relevant biomarkers for the reporting of clinical evidence
- Develop a lab-specific knowledgebase of interpretations that allow maximum re-use of interpretations and descriptions from one patient to the next
- Leverage the built-in Golden Helix CancerKB interpretation knowledgebase that covers many common genes and biomarkers
- When detecting inherited and not somatic variants in a patient, score and classify them using the ACMG guidelines and report as secondary germline findings
- Use the Oncogenicity scoring system for evaluating the impact of variants in cancer
- Customize your clinical report using Word to reflect your lab's preferences and branding
- Building on the success of VSClinical’s ACMG guidelines, the new VSClinical AMP guidelines enables new and existing labs to provide genetic tests for cancer efficiently and with a focus on delivering consistent and accurate results.
Exploring New Features and Clinical Reports in the ACMG Guideline WorkflowGolden Helix
For the past year, Golden Helix has been preparing a VarSeq release that includes ACMG Guidelines scoring and classification for not only single nucleotide variants but also copy number variants. In the past few months, our webcasts have introduced these guidelines and explored example CNVs that demonstrated the automated scoring of CNVs according to the new ACMG CNV Guidelines. However, there are many other new features and upgrades that have been incorporated into this VarSeq release. These upgrades have largely been driven by input from VarSeq users! That’s why I am very excited to explore these features together in the upcoming webcast “Exploring New Features and Clinical Reports in the ACMG Guideline Workflow”. In this webcast, we will walk through a workflow with SNVs and CNVs highlighting many of the new features and upgrades that will improve and streamline your ACMG workflow. Notably, we will see how these new features can also be incorporated into clinical reports.
Specifically, we will cover the following features:
New and improved ACMG Classifier algorithms
New and improved assessment catalogs for saving classifications and interpretations
New Project Options interface for creating patient evaluations
Now offering three new word-based clinical report templates
Inclusion of additional sections and features to the clinical reports
Enhanced report customization capability
Golden Helix's End-to-End Solution for Clinical LabsGolden Helix
In this webcast, we provide an overview of our complete end-to-end clinical stack. Initially, we walk through our powerful secondary analysis pipeline which allows you to call SNVs and CNVs. We then demonstrate how various types of CNVs are called and discuss metrics that express the confidence associated with each call.
From there, we show you our powerful tertiary analysis capabilities for gene panels, exome, and whole genome data. We show how our users can move seamlessly from the variant interpretation stage to a clinical report. Lastly, we demonstrate how our genetic data warehouse, VSWarehouse, can be used in the clinic. We also demonstrate various use cases and show how a comprehensive assessment catalog can be utilized to ensure consistent analysis across multiple labs.
We hope you enjoy our first presentation on Golden Helix's entire end-to-end solution for clinical labs!
Automating the ACMG Guidelines with VSClinicalGolden Helix
Clinical Genetic testing requires a complex analysis using the totality of our knowledge about the clinical relevance of a variant and a gene. This includes bioinformatic evidence as well as clinical evidence. The ACMG Guidelines provided a framework in which to score variants based on this evidence, and while some of those scoring criteria require close consultation of the clinical context for a given patient, much of it can be automated.
In this webcast, we review how VSClinical automates the ACMG scoring guidelines while integrating the collective lab expertise from previously classified variants and preferences about genes. We will cover:
Using the ACMG Auto Classifier as part the filtering strategy for gene panels and trio workflows
How gene preferences such as the default transcript, inheritance model, and disorder are updated and saved from VSClinical and used in all future analysis
How the per-variant recommendation engine builds on the auto-classification with descriptive reasons for answering each criterion yes or no
Using the auto-interpretation to present the evidence for all scored criteria in a human-readable paragraph
Working with VSClinical’s self-learning knowledgebase that incorporates previously classified variants and genes inform the interpretation of new variants!
Evaluating Copy Number Variants with VSClinical's New ACMG Guideline WorkflowGolden Helix
Golden Helix has been in close communication with the publishers of the ACMG guidelines and the ClinGen group to receive expert advice on how to interpret CNVs called on NGS data. These guidelines provide a robust set of rules for interpreting intragenic deletions and duplications, which is summarized into an intricate decision tree that is broken down into 80 distinct criteria. This complexity is further compounded by many important caveats, exceptions, and considerations known to many in the CNV clinical workspace but are not mentioned in the published guidelines. Fortunately, Golden Helix has spent long hours reading the guidelines, watching the webinars, reading the supplementary material, and working with collaborators to develop a comprehensive workflow to guide you through your clinical interpretation of CNVs. Herein, we are excited to cover more details into this novel ACMG CNV guideline interpretation workflow and demonstrate how intuitive this feature can be for your clinical pipeline. Specifically, we will cover:
The intricacies of the ACMG CNV Sample auto classifier
Unique annotations and algorithms
Adjustable metrics and parameters in the VSClinical ACMG interface
Rendering clinical reports
Extracting clinical value from next gen sequencingWinton Gibbons
It has become cliché in the clinical environment, and genetic sequencing realm, that there is a glut of sequence data. The conundrum is how to translate or transform the overabundance of data into clinically useful knowledge. This situation has only grown more acute since the introduction of next gen sequencing.
To arrive at the clinical knowledge, there needs to be a concentric series of integrated capabilities, and the necessary capacity. The core is of course the sequencing process itself, the IT tools to process it, and the human expertise. However, the essentials in the first two aspects, sequencing and IT, need to exist, and thereby create opportunities for organizations.
As there are numerable subtleties even within the essential capabilities, a single organization may not be able to develop all under one roof. Nor may certain abilities yet exist sufficiently. However, a complete ecosystem at best, or promising potential at worst, is still required.
The attached presentation illustrates the high-level transformation frameworks for this, and the subsequent translation of data to be clinically useful.
AMP-Based Variant Classification with VSClinicalGolden Helix
Evaluating somatic variants according to the cancer AMP guidelines can be an extensive process. In addition to the standard collection of all available, clinical evidence for any biomarkers, there is a need to define treatment options following final classification. Even the most adept clinicians familiar to the guidelines suffer from this arduous process and thus need a standardized approach for classifying, interpreting and reporting variants according to the AMP guidelines. VSClinical’s new AMP workflow alleviates these complexities by providing an automated workflow that captures and reports on all critical data present. With the VSClinical AMP workflow, users can also customize clinical reports to reflect your lab’s preferences and branding. This webcast will provide a simple AMP guideline-based demonstration from a user perspective with multiple examples of simple report customizations from the VSClinical interpretation hub.
What you will learn in this webcast:
How VSClinical integrates the tier system to evaluate somatic mutations according to the AMP guidelines, with a focus on SNPs, InDels, CNVs and fusions
Automating the AMP guidelines using Golden Helix CancerKB and lab-specific knowledge databases to streamline variant classifications
Multiple report examples to demonstrate simple Word-based report customization capability
Overall, VSClinical enables labs to test for both germline and somatic variants according to the ACMG and AMP guidelines in an automated fashion and allows users to obtain consistent and accurate results.
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP GuidelinesGolden Helix
Join us as we delve into VSWarehouse with a focus on our new capability of storing somatic variant projects and catalogs built for the AMP Guidelines within VSClinical.
We will also be demonstrating how VSWarehouse efficiently navigates through stored variants via the VSWarehouse Browser.
We hope you enjoy as we explore and leverage a comprehensive set of genomic data stored within VSWarehouse to ensure rapid workflow efficiency.
In this webcast, you will learn:
How to access the VSWarehouse terminal within VarSeq
Leverage the VSWarehouse genomic database in a VarSeq workflow
Explore the stored genomic data via the VSWarehouse Browser
You can read more about what this webcast covers over on our blog: https://blog.goldenhelix.com/vswarehouse-upgrade-somatic-variant-analysis-via-vsclinical-amp-guidelines/
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB UpdatesGolden Helix
Annotation sources are constantly evolving, sometimes quite literally overnight. This is especially true in the case of cancer databases. These ever-evolving annotation sources, coupled with increasing research publications, make it difficult to do variant analysis with up-to-date scientific knowledge. With the resources available to an individual clinician or single lab, this may even prove impossible. Fortunately, VSClinical provides access to the most current clinical annotation sources - automating scoring and interpreting variants according to the most recent ACMP and AMPO guidelines. This includes many fast-changing sources such as ClinVar and COSMIC, as well as expert-curated reviews of literature and the latest drug-labeling from regulatory bodies.
In this webcast, we demonstrate the automation of a cancer workflow with enhanced cancer annotations for somatic and germline cancer variants:
- Golden Helix’s own CancerKB database has been updated to include new interpretations for genes and biomarkers with AMP Tier Level I evidence for drug sensitivity, resistance, diagnostic, and prognostic information.
- We feature a new Golden Helix curated annotation source that automates the scoring of TP53 variants with the special rule specifications by ClinGen’s TP53 Expert Panel.
- The ClinGen Expert Curated Interpretation of Variants has always been available as an annotation source for VarSeq projects, but now the expert comments and interpretations can automatically be pulled into VSClinical and used for clinical reports.
This webcast walks through a hematological-focused cancer workflow that shows off the enhanced cancer annotations and CancerKB updates!
Using Golden Helix CancerKB to Accelerate NGS Cancer TestingGolden Helix
Next Generation Sequencing is being rapidly integrated into the oncology field. From the clinical perspective, both somatic and germline NGS results are informative for hereditary cancer risk and treatment strategies. There are numerous scattered resources that inform the clinical significance of a somatic mutation for a patient’s tumor type. Similarly, there are many FDA-approved anti-cancer agents and drugs with changing indications, and opportunities for off-label use. Even more, there are clinical trials all over the world that though they require specific genetic alterations for enrollment eligibility, they could provide more treatment options for cancer patients.
What’s the bottom line? It is certainly a huge undertaking to evaluate a gene or biomarker’s role in cancer or clinical significance. It requires sifting through trials that are relevant for the patient from the abundance of literature available, not to mention staying well-informed on new research as it is published.
Golden Helix CancerKB offers a solution. We demonstrate the application of CancerKB and how easy somatic variant analysis can be in VSClinical. Namely, I will deep dive into the following topics:
The process our expert curators use to produce high-quality cancer interpretations
Examples of complex biomarker interpretations simplified using CancerKB
Report content filled in by CancerKB, even for rare genes
Integrating customer feedback and the future of CancerKB
Before assessing the clinical significance of a somatic mutation, one must determine if the mutation is likely to be a driver mutation (i.e. a mutation that provides a selective growth advantage, thereby promoting cancer development). To aid clinicians in this process, VSClinical provides an oncogenicity scoring system, which uses a variety of metrics to classify a given somatic mutation into one of the following categories: oncogenic, likely oncogenic, benign, likely benign, or uncertain significance. This scoring system is heavily inspired by the ACMG Guidelines for the interpretation of germline mutations but has several important differences to make it more applicable in the context of somatic variant interpretation.
Our oncogenicity scoring system relies on an additive point system in which points are assigned to a given variant based on several criteria. Many of the criteria are shared by the ACMG Guidelines for germline variant interpretation, such as population frequency information, variant effect on protein function, and nearby pathogenic variants in catalogs such as ClinVar. However, other criteria are specific to the world of somatic variant interpretation. These include the variant’s presence in somatic catalogs such as COSMIC, the effect of other known oncogenic variants in the same gene, and the variant’s presence in known cancer hotspots or active binding sites. These criteria are combined by summing over the scores for all applicable scoring criteria. Scores exceeding 3 indicate an oncogenic or likely oncogenic classification, while scores falling below -3 indicate a benign or likely benign classification.
In this webcast, we discuss how each of these scoring criteria are combined to obtain an oncogenicity classification. This includes a discussion of the considerations taken into account during the development of this scoring system and a detailed analysis of several example mutations to illustrate the system in practice.
Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...Golden Helix
As exome sequencing continues to gain momentum as a comprehensive and affordable genetic test, many labs are considering the transition from their various targeted gene panels to a single comprehensive exome test. Along with the various challenges in small-variant analysis and interpretation of exomes, CNVs also require exome-specific considerations and strategies. In this webcast, we will review new capabilities and updated algorithms in the latest VarSeq release that will assist in any clinical exome sequencing workflow. Please join us in this webcast, as we review:
A new VS-CNV best-practice workflow with specialized features for calling CNVs on exomes and large panels with more precision, enhanced quality flags and additional outputs.
Enhanced analysis of variants found in exome sequencing, including non-coding clinically relevant RNA variants and mitochondrial variants
Additional CNV analysis capabilities such as CNV export and import as VCFs
The identification and interpretation of easily missed variants, such as those introducing novel splice-sites using the ACMG auto-classification and interpretation workflow
Strategies for incorporating disease-specific virtual gene panel lists into the filtering, quality and reporting capabilities of VSClinical
Exome sequence analysis is complex, and the process to define and validate a clinical exome test can be daunting. The VarSeq clinical suite has the flexibility and best practice workflows built-in to define and implement a repeatable and comprehensive workflow for CNVs detection and analysis by exome sequencing. We hope you can join this webinar to learn how to go from FASTQ to clinical reports for exome-based clinical tests.
Next-Generation Sequencing Analysis in VSClinicalGolden Helix
VarSeq is a tertiary analysis platform that allows users to filter and annotate NGS sequencing data to identify clinically relevant variants. Following this workflow, VSClinical can then be used to automate both germline and somatic variant analysis in accordance with the ACMG and AMP guidelines by using a variety of functional prediction models and clinical and reviewer-based annotations. Once variant or biomarker interpretations are completed, they can be rendered in a customizable clinical report and stored in an internal assessment catalog as an internal variant database repository. Together, implementation of VSClinical will promote increased lab throughput as well as accuracy and compliance with the ACMG and AMP guidelines, which in turn can save time and money. To show the capabilities of our software, this webcast will provide a demonstration of how to use VarSeq and VSClinical for the evaluation of both germline and somatic variants in accordance with the ACMG and AMP Guidelines.
In this webcast, we will cover:
- Filter logics for germline and somatic variants and selecting them into the VSClinical interface
- Capabilities of functional prediction and splice site algorithms for edge case variants
- The functionality of changing the clinically relevant transcript on variant interpretation
- Rendering a clinical report with germline and somatic variants with the inclusion of clinical trials
A User’s Perspective: ACMG Guidelines for CNVs in VSClinicalGolden Helix
Our last webcast introduced the newest features of VarSeq that will be included in our upcoming release. After a serious developmental effort, we are excited to announce one of these being the integration of ACMG Guidelines for CNVs!
VarSeq is not only the tertiary environment to filter through your imported SNVs and indels from any VCF file, but also includes robust and proven capabilities of CNV detection and clinical variant interpretation. With our upcoming release, users will be able to leverage an automated CNV ACMG classification filter that is paired with the CNV evaluation in the VSClinical interpretation hub. This webcast will expose attendees to literature reinforcing the quality of our CNV caller, as well as showing examples of CNV analysis to demonstrate how this tool can streamline the analysis process. In this webcast, we will cover:
Describing the new CNV guidelines and how Golden Helix tackles their complexity
Assessing CNV impact on Gene and Gene Dosage
Cited literature referencing the accuracy of VarSeq’s CNV calling
Product demonstrations of VSClinical’s CNV interpretation/classification and final report functionalities
Manually traversing the guidelines and classification process is fundamentally complex with multiple criteria considerations, collecting any necessary caveats, and bulk literature review just to name a few. It is our goal to simplify and streamline this process without losing user-control of final results or overlooking any crucial criteria components necessary for final classification. We hope you will join us to see how this is accomplished as we explore the ACMG CNV Guidelines within VSClinical from the user’s perspective!
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do trait analysis and association testing on large cohorts of samples in both humans and other species. As Next-Generation Sequencing of whole genomes becomes more affordable, large cohorts of Whole Genome Sequencing (WGS) samples are available to search for additional trait association signals that were not found in array-based testing. In fact, recent papers have shown that WGS analysis using advanced GREML (Genomic Relatedness Restricted Maximum Likelihood) techniques is able to outperform micro-array based GWAS methods in the analysis of complex traits and proportion of the trait heritability explained.
Our latest update release of SVS has expanded the exiting maximum likelihood and GRM methods to support these new techniques. We have also enhanced various other association testing and prediction methodologies. This webcast showcases:
- Newly supported analysis workflow for whole genome variants using LD binning and enhanced GBLUP analysis
- Enhanced gender correction using REML
- Additional capabilities for genomic prediction and phenotype prediction
We are continually improving our products based on our customer’s feedback. We hope you enjoy this recording highlighting the exciting new features and select enhancements we have made.
New & Improved COSMIC Database for NGS Cancer AnalysesGolden Helix
With Next-Gen Sequencing becoming a routine method of rapidly investigating cancer mutations, having access to accurate and large somatic variant catalogs is paramount. We at Golden Helix are excited to announce our newly released COSMIC 87 track. This updated version of the world's largest and most comprehensive somatic track provides a number of significant improvements. This includes not only an increase of ~1.1 million variants but also improvements on evidence accessibility and as always maintaining data quality. As a result of our 20+ years of bioinformatics experience, users have come to trust and rely on our data curation since our goal is to ensure highly efficient and accurate variant analysis. With this webcast, we are going to focus on the new capabilities users have when integrating COSMIC into their cancer workflow. We will also discuss the implications and value of relying on top data quality data curation maintained here at Golden Helix. Please join us as we seek to inform you on methods to optimize your cancer variant analysis!
- Discover new methods for managing clinical next-gen data with insights from Pfizer, Boston Children’s Hospital and AstraZeneca
- Uncover and critique the latest technologies out there for you to use in clinical trials. Mayo Clinic, Merck and Harvard Medical School let you into their trade secrets
- Hear the genomics strategies that Roche, Millennium and Regeneron are using for discovery and validation of clinically actionable biomarkers
-Bristol-Myers Squibb, Takeda and Partners Healthcare the role that NGS can play when implementing an effective strategy in the lab to speed up CDx development
- Learn how to integrate molecular details into medical decision making, with fresh data from Washington University School of Medicine and Genzyme
Clinical labs must have the ability to go from a collection of samples and associated variants to a professional report documenting a short list of clinically relevant variants. Cancer Gene Panels are a common clinical application for genetic tests. In this webcast we will show how VarSeq and VSReports can be used to go from an unfiltered variant file created by a secondary analysis pipeline to a report containing information about interesting variants.
This webcast will highlight VarSeq's support for Cancer Gene Panels and Tumor-Normal workflows by demonstrating:
• Variant, Region and Sample Quality Assurance
• Filtering to variants in targeted cancer genes relevant to the tumor type
• Summarizing variants in a clinical report
Introducing VSClinical AMP Guidelines: A Comprehensive Workflow for NGS Testi...Golden Helix
The individualized nature of tumors requires genomic testing for providing the best outcomes for patients. Next-Generation Sequencing enables the detection of small mutations, copy number changes, and common fusions affordably and with high precision. However, the interpretation of these detected variants is arduous without a comprehensive analytical workflow that can incorporate all the bioinformatics and clinical evidence involved in following the AMP guidelines for the scoring and reporting of somatic mutations.
Please join us as we reveal the AMP guidelines workflow support in VSClinical. We will cover the entire post-sequencing analytical workflow from FASTQ to clinical report, including:
- Apply the AMP Tiers to the available clinical evidence for Drug Sensitivity, Drug Response, Prognostics and Diagnostics
Support small mutations (SNPs, InDels) along with CNVs, fusions and wild-types as relevant biomarkers for the reporting of clinical evidence
- Develop a lab-specific knowledgebase of interpretations that allow maximum re-use of interpretations and descriptions from one patient to the next
- Leverage the built-in Golden Helix CancerKB interpretation knowledgebase that covers many common genes and biomarkers
- When detecting inherited and not somatic variants in a patient, score and classify them using the ACMG guidelines and report as secondary germline findings
- Use the Oncogenicity scoring system for evaluating the impact of variants in cancer
- Customize your clinical report using Word to reflect your lab's preferences and branding
- Building on the success of VSClinical’s ACMG guidelines, the new VSClinical AMP guidelines enables new and existing labs to provide genetic tests for cancer efficiently and with a focus on delivering consistent and accurate results.
Exploring New Features and Clinical Reports in the ACMG Guideline WorkflowGolden Helix
For the past year, Golden Helix has been preparing a VarSeq release that includes ACMG Guidelines scoring and classification for not only single nucleotide variants but also copy number variants. In the past few months, our webcasts have introduced these guidelines and explored example CNVs that demonstrated the automated scoring of CNVs according to the new ACMG CNV Guidelines. However, there are many other new features and upgrades that have been incorporated into this VarSeq release. These upgrades have largely been driven by input from VarSeq users! That’s why I am very excited to explore these features together in the upcoming webcast “Exploring New Features and Clinical Reports in the ACMG Guideline Workflow”. In this webcast, we will walk through a workflow with SNVs and CNVs highlighting many of the new features and upgrades that will improve and streamline your ACMG workflow. Notably, we will see how these new features can also be incorporated into clinical reports.
Specifically, we will cover the following features:
New and improved ACMG Classifier algorithms
New and improved assessment catalogs for saving classifications and interpretations
New Project Options interface for creating patient evaluations
Now offering three new word-based clinical report templates
Inclusion of additional sections and features to the clinical reports
Enhanced report customization capability
Golden Helix's End-to-End Solution for Clinical LabsGolden Helix
In this webcast, we provide an overview of our complete end-to-end clinical stack. Initially, we walk through our powerful secondary analysis pipeline which allows you to call SNVs and CNVs. We then demonstrate how various types of CNVs are called and discuss metrics that express the confidence associated with each call.
From there, we show you our powerful tertiary analysis capabilities for gene panels, exome, and whole genome data. We show how our users can move seamlessly from the variant interpretation stage to a clinical report. Lastly, we demonstrate how our genetic data warehouse, VSWarehouse, can be used in the clinic. We also demonstrate various use cases and show how a comprehensive assessment catalog can be utilized to ensure consistent analysis across multiple labs.
We hope you enjoy our first presentation on Golden Helix's entire end-to-end solution for clinical labs!
Automating the ACMG Guidelines with VSClinicalGolden Helix
Clinical Genetic testing requires a complex analysis using the totality of our knowledge about the clinical relevance of a variant and a gene. This includes bioinformatic evidence as well as clinical evidence. The ACMG Guidelines provided a framework in which to score variants based on this evidence, and while some of those scoring criteria require close consultation of the clinical context for a given patient, much of it can be automated.
In this webcast, we review how VSClinical automates the ACMG scoring guidelines while integrating the collective lab expertise from previously classified variants and preferences about genes. We will cover:
Using the ACMG Auto Classifier as part the filtering strategy for gene panels and trio workflows
How gene preferences such as the default transcript, inheritance model, and disorder are updated and saved from VSClinical and used in all future analysis
How the per-variant recommendation engine builds on the auto-classification with descriptive reasons for answering each criterion yes or no
Using the auto-interpretation to present the evidence for all scored criteria in a human-readable paragraph
Working with VSClinical’s self-learning knowledgebase that incorporates previously classified variants and genes inform the interpretation of new variants!
Evaluating Copy Number Variants with VSClinical's New ACMG Guideline WorkflowGolden Helix
Golden Helix has been in close communication with the publishers of the ACMG guidelines and the ClinGen group to receive expert advice on how to interpret CNVs called on NGS data. These guidelines provide a robust set of rules for interpreting intragenic deletions and duplications, which is summarized into an intricate decision tree that is broken down into 80 distinct criteria. This complexity is further compounded by many important caveats, exceptions, and considerations known to many in the CNV clinical workspace but are not mentioned in the published guidelines. Fortunately, Golden Helix has spent long hours reading the guidelines, watching the webinars, reading the supplementary material, and working with collaborators to develop a comprehensive workflow to guide you through your clinical interpretation of CNVs. Herein, we are excited to cover more details into this novel ACMG CNV guideline interpretation workflow and demonstrate how intuitive this feature can be for your clinical pipeline. Specifically, we will cover:
The intricacies of the ACMG CNV Sample auto classifier
Unique annotations and algorithms
Adjustable metrics and parameters in the VSClinical ACMG interface
Rendering clinical reports
Extracting clinical value from next gen sequencingWinton Gibbons
It has become cliché in the clinical environment, and genetic sequencing realm, that there is a glut of sequence data. The conundrum is how to translate or transform the overabundance of data into clinically useful knowledge. This situation has only grown more acute since the introduction of next gen sequencing.
To arrive at the clinical knowledge, there needs to be a concentric series of integrated capabilities, and the necessary capacity. The core is of course the sequencing process itself, the IT tools to process it, and the human expertise. However, the essentials in the first two aspects, sequencing and IT, need to exist, and thereby create opportunities for organizations.
As there are numerable subtleties even within the essential capabilities, a single organization may not be able to develop all under one roof. Nor may certain abilities yet exist sufficiently. However, a complete ecosystem at best, or promising potential at worst, is still required.
The attached presentation illustrates the high-level transformation frameworks for this, and the subsequent translation of data to be clinically useful.
AMP-Based Variant Classification with VSClinicalGolden Helix
Evaluating somatic variants according to the cancer AMP guidelines can be an extensive process. In addition to the standard collection of all available, clinical evidence for any biomarkers, there is a need to define treatment options following final classification. Even the most adept clinicians familiar to the guidelines suffer from this arduous process and thus need a standardized approach for classifying, interpreting and reporting variants according to the AMP guidelines. VSClinical’s new AMP workflow alleviates these complexities by providing an automated workflow that captures and reports on all critical data present. With the VSClinical AMP workflow, users can also customize clinical reports to reflect your lab’s preferences and branding. This webcast will provide a simple AMP guideline-based demonstration from a user perspective with multiple examples of simple report customizations from the VSClinical interpretation hub.
What you will learn in this webcast:
How VSClinical integrates the tier system to evaluate somatic mutations according to the AMP guidelines, with a focus on SNPs, InDels, CNVs and fusions
Automating the AMP guidelines using Golden Helix CancerKB and lab-specific knowledge databases to streamline variant classifications
Multiple report examples to demonstrate simple Word-based report customization capability
Overall, VSClinical enables labs to test for both germline and somatic variants according to the ACMG and AMP guidelines in an automated fashion and allows users to obtain consistent and accurate results.
VSWarehouse Upgrade: Somatic Variant Analysis via VSClinical AMP GuidelinesGolden Helix
Join us as we delve into VSWarehouse with a focus on our new capability of storing somatic variant projects and catalogs built for the AMP Guidelines within VSClinical.
We will also be demonstrating how VSWarehouse efficiently navigates through stored variants via the VSWarehouse Browser.
We hope you enjoy as we explore and leverage a comprehensive set of genomic data stored within VSWarehouse to ensure rapid workflow efficiency.
In this webcast, you will learn:
How to access the VSWarehouse terminal within VarSeq
Leverage the VSWarehouse genomic database in a VarSeq workflow
Explore the stored genomic data via the VSWarehouse Browser
You can read more about what this webcast covers over on our blog: https://blog.goldenhelix.com/vswarehouse-upgrade-somatic-variant-analysis-via-vsclinical-amp-guidelines/
Reduce Turn-Around with Enhanced Cancer Annotations and CancerKB UpdatesGolden Helix
Annotation sources are constantly evolving, sometimes quite literally overnight. This is especially true in the case of cancer databases. These ever-evolving annotation sources, coupled with increasing research publications, make it difficult to do variant analysis with up-to-date scientific knowledge. With the resources available to an individual clinician or single lab, this may even prove impossible. Fortunately, VSClinical provides access to the most current clinical annotation sources - automating scoring and interpreting variants according to the most recent ACMP and AMPO guidelines. This includes many fast-changing sources such as ClinVar and COSMIC, as well as expert-curated reviews of literature and the latest drug-labeling from regulatory bodies.
In this webcast, we demonstrate the automation of a cancer workflow with enhanced cancer annotations for somatic and germline cancer variants:
- Golden Helix’s own CancerKB database has been updated to include new interpretations for genes and biomarkers with AMP Tier Level I evidence for drug sensitivity, resistance, diagnostic, and prognostic information.
- We feature a new Golden Helix curated annotation source that automates the scoring of TP53 variants with the special rule specifications by ClinGen’s TP53 Expert Panel.
- The ClinGen Expert Curated Interpretation of Variants has always been available as an annotation source for VarSeq projects, but now the expert comments and interpretations can automatically be pulled into VSClinical and used for clinical reports.
This webcast walks through a hematological-focused cancer workflow that shows off the enhanced cancer annotations and CancerKB updates!
Using Golden Helix CancerKB to Accelerate NGS Cancer TestingGolden Helix
Next Generation Sequencing is being rapidly integrated into the oncology field. From the clinical perspective, both somatic and germline NGS results are informative for hereditary cancer risk and treatment strategies. There are numerous scattered resources that inform the clinical significance of a somatic mutation for a patient’s tumor type. Similarly, there are many FDA-approved anti-cancer agents and drugs with changing indications, and opportunities for off-label use. Even more, there are clinical trials all over the world that though they require specific genetic alterations for enrollment eligibility, they could provide more treatment options for cancer patients.
What’s the bottom line? It is certainly a huge undertaking to evaluate a gene or biomarker’s role in cancer or clinical significance. It requires sifting through trials that are relevant for the patient from the abundance of literature available, not to mention staying well-informed on new research as it is published.
Golden Helix CancerKB offers a solution. We demonstrate the application of CancerKB and how easy somatic variant analysis can be in VSClinical. Namely, I will deep dive into the following topics:
The process our expert curators use to produce high-quality cancer interpretations
Examples of complex biomarker interpretations simplified using CancerKB
Report content filled in by CancerKB, even for rare genes
Integrating customer feedback and the future of CancerKB
Before assessing the clinical significance of a somatic mutation, one must determine if the mutation is likely to be a driver mutation (i.e. a mutation that provides a selective growth advantage, thereby promoting cancer development). To aid clinicians in this process, VSClinical provides an oncogenicity scoring system, which uses a variety of metrics to classify a given somatic mutation into one of the following categories: oncogenic, likely oncogenic, benign, likely benign, or uncertain significance. This scoring system is heavily inspired by the ACMG Guidelines for the interpretation of germline mutations but has several important differences to make it more applicable in the context of somatic variant interpretation.
Our oncogenicity scoring system relies on an additive point system in which points are assigned to a given variant based on several criteria. Many of the criteria are shared by the ACMG Guidelines for germline variant interpretation, such as population frequency information, variant effect on protein function, and nearby pathogenic variants in catalogs such as ClinVar. However, other criteria are specific to the world of somatic variant interpretation. These include the variant’s presence in somatic catalogs such as COSMIC, the effect of other known oncogenic variants in the same gene, and the variant’s presence in known cancer hotspots or active binding sites. These criteria are combined by summing over the scores for all applicable scoring criteria. Scores exceeding 3 indicate an oncogenic or likely oncogenic classification, while scores falling below -3 indicate a benign or likely benign classification.
In this webcast, we discuss how each of these scoring criteria are combined to obtain an oncogenicity classification. This includes a discussion of the considerations taken into account during the development of this scoring system and a detailed analysis of several example mutations to illustrate the system in practice.
Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Ca...Golden Helix
As exome sequencing continues to gain momentum as a comprehensive and affordable genetic test, many labs are considering the transition from their various targeted gene panels to a single comprehensive exome test. Along with the various challenges in small-variant analysis and interpretation of exomes, CNVs also require exome-specific considerations and strategies. In this webcast, we will review new capabilities and updated algorithms in the latest VarSeq release that will assist in any clinical exome sequencing workflow. Please join us in this webcast, as we review:
A new VS-CNV best-practice workflow with specialized features for calling CNVs on exomes and large panels with more precision, enhanced quality flags and additional outputs.
Enhanced analysis of variants found in exome sequencing, including non-coding clinically relevant RNA variants and mitochondrial variants
Additional CNV analysis capabilities such as CNV export and import as VCFs
The identification and interpretation of easily missed variants, such as those introducing novel splice-sites using the ACMG auto-classification and interpretation workflow
Strategies for incorporating disease-specific virtual gene panel lists into the filtering, quality and reporting capabilities of VSClinical
Exome sequence analysis is complex, and the process to define and validate a clinical exome test can be daunting. The VarSeq clinical suite has the flexibility and best practice workflows built-in to define and implement a repeatable and comprehensive workflow for CNVs detection and analysis by exome sequencing. We hope you can join this webinar to learn how to go from FASTQ to clinical reports for exome-based clinical tests.
Next-Generation Sequencing Analysis in VSClinicalGolden Helix
VarSeq is a tertiary analysis platform that allows users to filter and annotate NGS sequencing data to identify clinically relevant variants. Following this workflow, VSClinical can then be used to automate both germline and somatic variant analysis in accordance with the ACMG and AMP guidelines by using a variety of functional prediction models and clinical and reviewer-based annotations. Once variant or biomarker interpretations are completed, they can be rendered in a customizable clinical report and stored in an internal assessment catalog as an internal variant database repository. Together, implementation of VSClinical will promote increased lab throughput as well as accuracy and compliance with the ACMG and AMP guidelines, which in turn can save time and money. To show the capabilities of our software, this webcast will provide a demonstration of how to use VarSeq and VSClinical for the evaluation of both germline and somatic variants in accordance with the ACMG and AMP Guidelines.
In this webcast, we will cover:
- Filter logics for germline and somatic variants and selecting them into the VSClinical interface
- Capabilities of functional prediction and splice site algorithms for edge case variants
- The functionality of changing the clinically relevant transcript on variant interpretation
- Rendering a clinical report with germline and somatic variants with the inclusion of clinical trials
A User’s Perspective: ACMG Guidelines for CNVs in VSClinicalGolden Helix
Our last webcast introduced the newest features of VarSeq that will be included in our upcoming release. After a serious developmental effort, we are excited to announce one of these being the integration of ACMG Guidelines for CNVs!
VarSeq is not only the tertiary environment to filter through your imported SNVs and indels from any VCF file, but also includes robust and proven capabilities of CNV detection and clinical variant interpretation. With our upcoming release, users will be able to leverage an automated CNV ACMG classification filter that is paired with the CNV evaluation in the VSClinical interpretation hub. This webcast will expose attendees to literature reinforcing the quality of our CNV caller, as well as showing examples of CNV analysis to demonstrate how this tool can streamline the analysis process. In this webcast, we will cover:
Describing the new CNV guidelines and how Golden Helix tackles their complexity
Assessing CNV impact on Gene and Gene Dosage
Cited literature referencing the accuracy of VarSeq’s CNV calling
Product demonstrations of VSClinical’s CNV interpretation/classification and final report functionalities
Manually traversing the guidelines and classification process is fundamentally complex with multiple criteria considerations, collecting any necessary caveats, and bulk literature review just to name a few. It is our goal to simplify and streamline this process without losing user-control of final results or overlooking any crucial criteria components necessary for final classification. We hope you will join us to see how this is accomplished as we explore the ACMG CNV Guidelines within VSClinical from the user’s perspective!
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do trait analysis and association testing on large cohorts of samples in both humans and other species. As Next-Generation Sequencing of whole genomes becomes more affordable, large cohorts of Whole Genome Sequencing (WGS) samples are available to search for additional trait association signals that were not found in array-based testing. In fact, recent papers have shown that WGS analysis using advanced GREML (Genomic Relatedness Restricted Maximum Likelihood) techniques is able to outperform micro-array based GWAS methods in the analysis of complex traits and proportion of the trait heritability explained.
Our latest update release of SVS has expanded the exiting maximum likelihood and GRM methods to support these new techniques. We have also enhanced various other association testing and prediction methodologies. This webcast showcases:
- Newly supported analysis workflow for whole genome variants using LD binning and enhanced GBLUP analysis
- Enhanced gender correction using REML
- Additional capabilities for genomic prediction and phenotype prediction
We are continually improving our products based on our customer’s feedback. We hope you enjoy this recording highlighting the exciting new features and select enhancements we have made.
New & Improved COSMIC Database for NGS Cancer AnalysesGolden Helix
With Next-Gen Sequencing becoming a routine method of rapidly investigating cancer mutations, having access to accurate and large somatic variant catalogs is paramount. We at Golden Helix are excited to announce our newly released COSMIC 87 track. This updated version of the world's largest and most comprehensive somatic track provides a number of significant improvements. This includes not only an increase of ~1.1 million variants but also improvements on evidence accessibility and as always maintaining data quality. As a result of our 20+ years of bioinformatics experience, users have come to trust and rely on our data curation since our goal is to ensure highly efficient and accurate variant analysis. With this webcast, we are going to focus on the new capabilities users have when integrating COSMIC into their cancer workflow. We will also discuss the implications and value of relying on top data quality data curation maintained here at Golden Helix. Please join us as we seek to inform you on methods to optimize your cancer variant analysis!
- Discover new methods for managing clinical next-gen data with insights from Pfizer, Boston Children’s Hospital and AstraZeneca
- Uncover and critique the latest technologies out there for you to use in clinical trials. Mayo Clinic, Merck and Harvard Medical School let you into their trade secrets
- Hear the genomics strategies that Roche, Millennium and Regeneron are using for discovery and validation of clinically actionable biomarkers
-Bristol-Myers Squibb, Takeda and Partners Healthcare the role that NGS can play when implementing an effective strategy in the lab to speed up CDx development
- Learn how to integrate molecular details into medical decision making, with fresh data from Washington University School of Medicine and Genzyme
Updated Agenda- CRISPR Congress in Berlin, 24-26 October 2016Diane McKenna
The Only Industry Event Solely Dedicated to Optimising the Applications CRISPR Precision Genome Editing in Europe.
Overcome key specificity, efficiency & delivery challenges to pioneer drug discovery, biomedical research and therapeutic applications of precision genome engineering. With customisation of CRISPR design paramount, join leading biopharma and academic figureheads as they reveal advanced methodology, strategies and clinical timelines to fulfil the revolutionary promise of precision genome editing.
According to a 2016 Nature survey, more than 70% of researchers have failed to reproduce another scientist’s experiments. To solve the reproducibility problem, the research community demands high-quality biobanks to deliver fit-for-purpose biospecimens – key pillars advancing science in medicine. Precision for Medicine is a global leader in supplying diverse, high quality, IRB-approved, clinically annotated, ready-to-ship human biospecimens.
This talk provides an insider’s look into Precision for Medicine’s variant-rich biobank showcasing biospecimen types, highlighting usage, custom collection solutions and disease-matched control sets across multiple therapeutic areas. Precision for Medicine’s biorepository contains diverse, genetically characterized specimens validated using various NGS assays and platforms.
Described in this talk are just some of the sample types, screening methods, and subsequently the integrated QuartzBio database of variants found. The speakers also discuss Precision for Medicine’s partnership capabilities, such as for supporting companion diagnostic development including inter-laboratory reproducibility, validation kit assembly and prospective collections for matched tissue types, minimal residual disease, and clinical trial enrollment.
Key Topics Include:
- Gain a broad understanding of Precision for Medicine, Biospecimen Solutions variant-rich biobank contents pertaining to different therapeutic areas
- Become familiar with fit-for-purpose human biospecimens, their diverse types and appropriate uses
- Become acquainted with the biospecimen characterization data available from Precision for
Medicine, Biospecimen Solutions
- Discover the various partnership options for sample and patient screening for R&D and CDx development and clinical trial enrollment
Roundup of This Year's AACC Meeting in AtlantaBruce Carlson
The American Association of Clinical Chemistry was held this year in Atlanta, GA. Kalorama was at the meeting and notes several developments, with a particular focus on point-of-care.
Strand featured in CIO Review: Pharma and Life Science Special edition - July 2014
Strand Genomics Inc recognised by CIO Review as one among 20 most promising Tech solution providers to Pharma and Life science industry 2014
Precision Medicine & Biomarkers Leaders Summit - Boston USA - 7th & 8th MayTony Couch
This expanding series attracts the leading authorities worldwide working in companion diagnostics, biomarkers, immuno-oncology, liquid biopsies, AI and other facets of precision medicine. It has been praised for its stimulating, interactive and engaging environment where it brings together a multi-disciplined community of researchers, leaders and innovators whose aim is to develop groundbreaking and impactful treatments for patients.
Precision Medicine- Growth Opportunities for Genomics TechnologiesWilliam Baird
Made at the 4th Global Precision Medicine and Biomarkers Leaders Summit: Europe by Nitin Naik. For more information visit http://www.global-engage.com/wp-content/uploads/2017/04/Global-Precision-Medicine-Biomarkers-Europe-2017.pdf. Better understanding of disease heterogeneity and identification of novel targets will expand precision medicine applications beyond oncology and foster collaboration between pharmaceutical companies, diagnostic manufacturers, payers and providers to develop new products and services. In next three years, Clinical sequencing technologies and NGS informatics & services represent the largest growth potential. Other emerging technologies such
as liquid biopsy and point-of-care testing technologies will start to compete against established NGS space for precision diagnostics. This briefing will provide strategic insights into growth opportunities related to Genomics, Molecular Diagnostics, and Sequencing Technologies shaping the future of Global Precision Medicine industry. It will specifically highlight global & regional initiatives, game changing companies and disruptive technologies (big data, cloud, predictive analytics)
shaping new business models.
The Pistoia Alliance is examining the challenges of the Faster Safe Companion Diagnostics (CDx) by Aligning Discovery & Clinical Data in the Regulatory Domain.
The slides discuss whether the data standards used in the research environment be aligned better with the data standards used in the regulated environment? If so, the time and cost of the development of NGS-based CDx could be reduced.
Next Generation Companion Diagnostics; Adoption, Drivers, and Moderators of N...Andrew Aijian
Analysis and synthesis of a pulse survey conducted across >140 oncologists, pathologists, and lab directors regarding current adoption and trends associated with emerging oncology biomarkers and companion diagnostics (CDx), with an emphasis on next-generation sequencing (NGS)-based CDx.
Customized Oncology Development Solutions: Clinical Trials Designed Around You®Covance
Oncology is one of the most research-intensive therapeutic areas, yet no two development programs are the same. No two trials are the same. Each one calls for a customized strategy and distinct trial management approach. Covance develops fit-for-purpose solutions Designed Around You® that enable more efficient clinical trials and focus on what is most valuable to your organization.
Precision Medicine & Biomarkers Leaders Summit - Boston USA - 7th & 8th MayTony Couch
Global Engage is pleased to announce the 2018 Precision Medicine & Biomarkers Leaders Summit USA taking place on May 7-8th in Boston, MA. The event is part of our highly successful Drug Discovery Series which includes conferences on Biologics, Medicinal Chemistry, NASH, Pharmaceutical R&D IT and the Human Microbiome amongst others. It is also the sister meeting of the European Precision Medicine Summit which has run successfully since 2013.
Precision Medicine & Biomarkers Leaders Summit - Boston USA - 7th & 8th MayTony Couch
Tracks focus on R&D strategies, Biomarker development, Immuno-oncology, CDx development, AI and Big data analysis and approaches – Attending this Summit will provide you with the opportunity to mix and interact with experts working in all facets of Precision Medicine through the individual, panel and roundtable discussions on offer.
Empowering ACOs: Leveraging Quality Management Tools for MIPS and BeyondHealth Catalyst
Join us as we delve into the crucial realm of quality reporting for MSSP (Medicare Shared Savings Program) Accountable Care Organizations (ACOs).
In this session, we will explore how a robust quality management solution can empower your organization to meet regulatory requirements and improve processes for MIPS reporting and internal quality programs. Learn how our MeasureAble application enables compliance and fosters continuous improvement.
India Clinical Trials Market: Industry Size and Growth Trends [2030] Analyzed...Kumar Satyam
According to TechSci Research report, "India Clinical Trials Market- By Region, Competition, Forecast & Opportunities, 2030F," the India Clinical Trials Market was valued at USD 2.05 billion in 2024 and is projected to grow at a compound annual growth rate (CAGR) of 8.64% through 2030. The market is driven by a variety of factors, making India an attractive destination for pharmaceutical companies and researchers. India's vast and diverse patient population, cost-effective operational environment, and a large pool of skilled medical professionals contribute significantly to the market's growth. Additionally, increasing government support in streamlining regulations and the growing prevalence of lifestyle diseases further propel the clinical trials market.
Growing Prevalence of Lifestyle Diseases
The rising incidence of lifestyle diseases such as diabetes, cardiovascular diseases, and cancer is a major trend driving the clinical trials market in India. These conditions necessitate the development and testing of new treatment methods, creating a robust demand for clinical trials. The increasing burden of these diseases highlights the need for innovative therapies and underscores the importance of India as a key player in global clinical research.
Defecation
Normal defecation begins with movement in the left colon, moving stool toward the anus. When stool reaches the rectum, the distention causes relaxation of the internal sphincter and an awareness of the need to defecate. At the time of defecation, the external sphincter relaxes, and abdominal muscles contract, increasing intrarectal pressure and forcing the stool out
The Valsalva maneuver exerts pressure to expel faeces through a voluntary contraction of the abdominal muscles while maintaining forced expiration against a closed airway. Patients with cardiovascular disease, glaucoma, increased intracranial pressure, or a new surgical wound are at greater risk for cardiac dysrhythmias and elevated blood pressure with the Valsalva maneuver and need to avoid straining to pass the stool.
Normal defecation is painless, resulting in passage of soft, formed stool
CONSTIPATION
Constipation is a symptom, not a disease. Improper diet, reduced fluid intake, lack of exercise, and certain medications can cause constipation. For example, patients receiving opiates for pain after surgery often require a stool softener or laxative to prevent constipation. The signs of constipation include infrequent bowel movements (less than every 3 days), difficulty passing stools, excessive straining, inability to defecate at will, and hard feaces
IMPACTION
Fecal impaction results from unrelieved constipation. It is a collection of hardened feces wedged in the rectum that a person cannot expel. In cases of severe impaction the mass extends up into the sigmoid colon.
DIARRHEA
Diarrhea is an increase in the number of stools and the passage of liquid, unformed feces. It is associated with disorders affecting digestion, absorption, and secretion in the GI tract. Intestinal contents pass through the small and large intestine too quickly to allow for the usual absorption of fluid and nutrients. Irritation within the colon results in increased mucus secretion. As a result, feces become watery, and the patient is unable to control the urge to defecate. Normally an anal bag is safe and effective in long-term treatment of patients with fecal incontinence at home, in hospice, or in the hospital. Fecal incontinence is expensive and a potentially dangerous condition in terms of contamination and risk of skin ulceration
HEMORRHOIDS
Hemorrhoids are dilated, engorged veins in the lining of the rectum. They are either external or internal.
FLATULENCE
As gas accumulates in the lumen of the intestines, the bowel wall stretches and distends (flatulence). It is a common cause of abdominal fullness, pain, and cramping. Normally intestinal gas escapes through the mouth (belching) or the anus (passing of flatus)
FECAL INCONTINENCE
Fecal incontinence is the inability to control passage of feces and gas from the anus. Incontinence harms a patient’s body image
PREPARATION AND GIVING OF LAXATIVESACCORDING TO POTTER AND PERRY,
An enema is the instillation of a solution into the rectum and sig
ICH Guidelines for Pharmacovigilance.pdfNEHA GUPTA
The "ICH Guidelines for Pharmacovigilance" PDF provides a comprehensive overview of the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) guidelines related to pharmacovigilance. These guidelines aim to ensure that drugs are safe and effective for patients by monitoring and assessing adverse effects, ensuring proper reporting systems, and improving risk management practices. The document is essential for professionals in the pharmaceutical industry, regulatory authorities, and healthcare providers, offering detailed procedures and standards for pharmacovigilance activities to enhance drug safety and protect public health.
Medical Technology Tackles New Health Care Demand - Research Report - March 2...pchutichetpong
M Capital Group (“MCG”) predicts that with, against, despite, and even without the global pandemic, the medical technology (MedTech) industry shows signs of continuous healthy growth, driven by smaller, faster, and cheaper devices, growing demand for home-based applications, technological innovation, strategic acquisitions, investments, and SPAC listings. MCG predicts that this should reflects itself in annual growth of over 6%, well beyond 2028.
According to Chris Mouchabhani, Managing Partner at M Capital Group, “Despite all economic scenarios that one may consider, beyond overall economic shocks, medical technology should remain one of the most promising and robust sectors over the short to medium term and well beyond 2028.”
There is a movement towards home-based care for the elderly, next generation scanning and MRI devices, wearable technology, artificial intelligence incorporation, and online connectivity. Experts also see a focus on predictive, preventive, personalized, participatory, and precision medicine, with rising levels of integration of home care and technological innovation.
The average cost of treatment has been rising across the board, creating additional financial burdens to governments, healthcare providers and insurance companies. According to MCG, cost-per-inpatient-stay in the United States alone rose on average annually by over 13% between 2014 to 2021, leading MedTech to focus research efforts on optimized medical equipment at lower price points, whilst emphasizing portability and ease of use. Namely, 46% of the 1,008 medical technology companies in the 2021 MedTech Innovator (“MTI”) database are focusing on prevention, wellness, detection, or diagnosis, signaling a clear push for preventive care to also tackle costs.
In addition, there has also been a lasting impact on consumer and medical demand for home care, supported by the pandemic. Lockdowns, closure of care facilities, and healthcare systems subjected to capacity pressure, accelerated demand away from traditional inpatient care. Now, outpatient care solutions are driving industry production, with nearly 70% of recent diagnostics start-up companies producing products in areas such as ambulatory clinics, at-home care, and self-administered diagnostics.
The dimensions of healthcare quality refer to various attributes or aspects that define the standard of healthcare services. These dimensions are used to evaluate, measure, and improve the quality of care provided to patients. A comprehensive understanding of these dimensions ensures that healthcare systems can address various aspects of patient care effectively and holistically. Dimensions of Healthcare Quality and Performance of care include the following; Appropriateness, Availability, Competence, Continuity, Effectiveness, Efficiency, Efficacy, Prevention, Respect and Care, Safety as well as Timeliness.
CRISPR-Cas9, a revolutionary gene-editing tool, holds immense potential to reshape medicine, agriculture, and our understanding of life. But like any powerful tool, it comes with ethical considerations.
Unveiling CRISPR: This naturally occurring bacterial defense system (crRNA & Cas9 protein) fights viruses. Scientists repurposed it for precise gene editing (correction, deletion, insertion) by targeting specific DNA sequences.
The Promise: CRISPR offers exciting possibilities:
Gene Therapy: Correcting genetic diseases like cystic fibrosis.
Agriculture: Engineering crops resistant to pests and harsh environments.
Research: Studying gene function to unlock new knowledge.
The Peril: Ethical concerns demand attention:
Off-target Effects: Unintended DNA edits can have unforeseen consequences.
Eugenics: Misusing CRISPR for designer babies raises social and ethical questions.
Equity: High costs could limit access to this potentially life-saving technology.
The Path Forward: Responsible development is crucial:
International Collaboration: Clear guidelines are needed for research and human trials.
Public Education: Open discussions ensure informed decisions about CRISPR.
Prioritize Safety and Ethics: Safety and ethical principles must be paramount.
CRISPR offers a powerful tool for a better future, but responsible development and addressing ethical concerns are essential. By prioritizing safety, fostering open dialogue, and ensuring equitable access, we can harness CRISPR's power for the benefit of all. (2998 characters)
Antibiotic Stewardship by Anushri Srivastava.pptxAnushriSrivastav
Stewardship is the act of taking good care of something.
Antimicrobial stewardship is a coordinated program that promotes the appropriate use of antimicrobials (including antibiotics), improves patient outcomes, reduces microbial resistance, and decreases the spread of infections caused by multidrug-resistant organisms.
WHO launched the Global Antimicrobial Resistance and Use Surveillance System (GLASS) in 2015 to fill knowledge gaps and inform strategies at all levels.
ACCORDING TO apic.org,
Antimicrobial stewardship is a coordinated program that promotes the appropriate use of antimicrobials (including antibiotics), improves patient outcomes, reduces microbial resistance, and decreases the spread of infections caused by multidrug-resistant organisms.
ACCORDING TO pewtrusts.org,
Antibiotic stewardship refers to efforts in doctors’ offices, hospitals, long term care facilities, and other health care settings to ensure that antibiotics are used only when necessary and appropriate
According to WHO,
Antimicrobial stewardship is a systematic approach to educate and support health care professionals to follow evidence-based guidelines for prescribing and administering antimicrobials
In 1996, John McGowan and Dale Gerding first applied the term antimicrobial stewardship, where they suggested a causal association between antimicrobial agent use and resistance. They also focused on the urgency of large-scale controlled trials of antimicrobial-use regulation employing sophisticated epidemiologic methods, molecular typing, and precise resistance mechanism analysis.
Antimicrobial Stewardship(AMS) refers to the optimal selection, dosing, and duration of antimicrobial treatment resulting in the best clinical outcome with minimal side effects to the patients and minimal impact on subsequent resistance.
According to the 2019 report, in the US, more than 2.8 million antibiotic-resistant infections occur each year, and more than 35000 people die. In addition to this, it also mentioned that 223,900 cases of Clostridoides difficile occurred in 2017, of which 12800 people died. The report did not include viruses or parasites
VISION
Being proactive
Supporting optimal animal and human health
Exploring ways to reduce overall use of antimicrobials
Using the drugs that prevent and treat disease by killing microscopic organisms in a responsible way
GOAL
to prevent the generation and spread of antimicrobial resistance (AMR). Doing so will preserve the effectiveness of these drugs in animals and humans for years to come.
being to preserve human and animal health and the effectiveness of antimicrobial medications.
to implement a multidisciplinary approach in assembling a stewardship team to include an infectious disease physician, a clinical pharmacist with infectious diseases training, infection preventionist, and a close collaboration with the staff in the clinical microbiology laboratory
to prevent antimicrobial overuse, misuse and abuse.
to minimize the developme
R3 Stem Cells and Kidney Repair A New Horizon in Nephrology.pptxR3 Stem Cell
R3 Stem Cells and Kidney Repair: A New Horizon in Nephrology" explores groundbreaking advancements in the use of R3 stem cells for kidney disease treatment. This insightful piece delves into the potential of these cells to regenerate damaged kidney tissue, offering new hope for patients and reshaping the future of nephrology.
Explore our infographic on 'Essential Metrics for Palliative Care Management' which highlights key performance indicators crucial for enhancing the quality and efficiency of palliative care services.
This visual guide breaks down important metrics across four categories: Patient-Centered Metrics, Care Efficiency Metrics, Quality of Life Metrics, and Staff Metrics. Each section is designed to help healthcare professionals monitor and improve care delivery for patients facing serious illnesses. Understand how to implement these metrics in your palliative care practices for better outcomes and higher satisfaction levels.
Optimizing the Output of Your Molecular Pathology Laboratory
1. 1 | April 24, 2018www.pieriandx.comwww.pieriandx.com
BG Jones
Senior Vice President, Business Development
Optimizing the
Output of Your Molecular
Pathology Laboratory
With the Right Mix of Technology and Services
2. 2 | April 24, 2018www.pieriandx.com
Webinar
Topics
1
3
4
Industry Trends and Challenges
Actionable Intelligence
Complete Clinical Genomics Solutions
2 PierianDx Customer Experiences
3. 3 | April 24, 2018www.pieriandx.com
Industry
Trends & Challenges
4. 4 | April 24, 2018www.pieriandx.com
Strong growth underway
Molecular diagnostic market size is
projected to reach $10.12 Billion from
$6.54 Billion in 2016, at a CAGR of 9.1%.
As most diagnostic tests are performed
in-house, the hospital & academic
laboratories segment is expected to
dominate the market.
Source: ReportsnReports
Molecular Diagnostics
Market
In-House Testing
2016
Clinical genetic testing labs
US Market
2017 NGS Testing
272
5.5
MM Clinical genetic tests conducted
$6.5B
$10.1B
2021
Global oncology based molecular
diagnostics market is expected to reach
$3.39 Billion by 2022.
Sequencing is estimated to be the
fastest growing segment with CAGR
estimated at over 19%.
Source: Grand View Research
Next Generation Sequencing
Source: Epstein Health
Trends - Market Size
1.1
MM NGS tests conducted
5. 5 | April 20, 2018www.pieriandx.com
Industry milestones and trends
The Inflection Point
CMS finalized a National
Coverage Determination that
covers diagnostic laboratory
tests using Next Generation
Sequencing (NGS) for patients
with advanced cancer (i.e.,
recurrent, metastatic, relapsed,
refractory, or stages III or IV
cancer).
CMS.gov
NGS Reimbursement
CMS National Coverage
Gene therapy
Kyrmriah is the first gene therapy
approved in the US, to treat
children with advanced leukemia.
Immunotherapy
Merck’s Keytruda is the first
immunotherapy treatment
approved for all solid tumors
based on a genomic biomarker.
FDA Approval
Sep’17
Aug’17
Nov’17
Nov’17
Somatic cancer tests
Oncomine Dx, MSK-IMPACT, and
FoundationOne CDx are the
first NGS tumor profiling assays
to gain FDA approval.
Mar’18
Jun’17
6. 6 | April 24, 2018www.pieriandx.com
In-House Testing
NGS Processing Challenges
Amount of data to curate and
interpret from publications
Rapidly changing therapies,
guidelines, clinical trials
Scarcity of genomic analysts
Dynamic workflow needed
Growing number of assays from
multiple vendors
BM Good, Genome Biology 2014
7. 7 | April 24, 2018www.pieriandx.com
Interpretation of the clinical significance of
genomic alterations remains the most severe
bottleneck preventing the realization of
personalized medicine in cancer.
Organizing knowledge to enable personalization of
medicine in cancer. Genome Biology 2014
In-House Testing
Interpretation Bottleneck
‟
BM Good, Genome Biology 2014
8. 8 | April 24, 2018www.pieriandx.com
PierianDx
Overview
9. 9 | April 24, 2018www.pieriandx.com
Pioneers of Precision Medicine
Leaders in Clinical Genomics
www.pieriandx.com
Originated at Washington University in 2011
65+ Employees
45+ Customers in Sharing Network
25+ Validated Assays
7,800+ Shared Clinical Interpretations
CLIA Certified, CAP Distributive Model
9 | April 24, 2018
10. 10 | April 24, 2018www.pieriandx.com
Prev: Professor and Director at
Washington University
Curr: CAP Molecular Oncology
Committee, Genomic Medicine
Resource Committee, CAP Inspector
Rakesh Nagarajan,
MD, PhD
Chief Executive Officer
Biomedical Informatics
Clinical Leadership
Experience Matters
Prev: Senior Medical Director
GE-Clarient, Roche Molecular Systems,
MD Anderson
Shalini Verma, MD, FCAP
Chief Medical Officer
Molecular Pathology
Prev: GM, GeneInsight
at Sunquest Information Systems
Chris Callahan, MBA
Chief Commercial Officer
Commercial Growth
www.pieriandx.com
Prev: Director Policy/Finance, NIH, Mass. Gen.
Director of Clinical Operations, Washington
University
Andy Bredemeyer, PhD
Director, Customer Operations
Clinical Operations
11. 11 | April 24, 2018www.pieriandx.com
Our Partners
Innovators in Precision Medicine
Top 50 Cancer Hospitals*
Leverage the expertise of your peers and
pioneers in somatic oncology.
* 2018 US News & World Report Top 50 Cancer Hospitals.
12. 12 | April 24, 2018www.pieriandx.com
Precision Oncology
Success Study “Working with PierianDx has been an ideal partnership.
They have been with us since the early onset of our
program, providing both the technology and services that
allowed us to ramp our program much faster.”
— Dr. Anthony Magliocco
Exec. Director, Esoteric Laboratory Services
#18
2 NGS tests go live
1st patient cases run
Moffitt partners with
PierianDx
PierianDx Lab Services
added, increases
Moffitt’s capacity
Interpretation Services
added
NGS informatics
upgraded
1st clinical
TruSight™ Tumor 170
assay goes live
(Moffitt NGS STAR)
#9
www.pieriandx.com
May 2014 Oct 2014 Nov 2015 Jan 2016 Jan 2017 Mar 2018
13. 13 | April 24, 2018www.pieriandx.com
Complete Clinical
Genomics Solutions
14. 14 | April 24, 2018www.pieriandx.com
An Integrated Approach
Laboratory Enablers
Laboratory Services
Turnkey, validated assays and informatics.
Minimizes expense of implementation.
Clinical Genomics Workspace
All-in-one informatics and reporting software.
Seamlessly integrated with EMR and Lab IS.
Medical & Scientific Services
Complete clinical support
Experienced team to fast-track growth
Content Sharing Network
The largest opt-in content sharing network
Greater precision in advanced cancer care.
15. 15 | April 24, 2018www.pieriandx.com
Integrated Platform
Complete Clinical Support
✓PierianDx Solutions
Outreach,
Planning &
Assay
Validation
Sequencing
Variant
Calling
(Bioinformatic
Pipelines)
Variant
Annotation &
Classification
Data
Visualization
& QC Metrics
Final Report &
Medical
Director Sign-
out
Data
Integration
EMR, 3rd
Party
People SoftwareWet Lab
Clinical
Interpretation
& Reporting
✓✓ ✓✓ ✓ ✓ ✓ ✓
16. 16 | April 24, 2018www.pieriandx.com
All Bases Covered
Implemented Assays
Assay Vendor Variant Types Input Files
Amplicon
VariantPlex Myeloid Archer SNVs and indels TSV from Archer
VariantPlex BRCA1/BRCA2 Archer SNVs and indels VCF, BAM,BAI
TruSight Myeloid Illumina SNVs and indels FASTQ, BAM, VCF
TruSight Tumor 15 Illumina SNVs and indels FASTQ, BAM, VCF
TruSight Tumor 26 Illumina SNVs and indels FASTQ, BAM, VCF
TruSeq Cancer Amplicon (TSCA) Illumina SNVs and indels FASTQ, BAM, VCF
BRCA1/BRCA2 (AFP2 assay) Illumina SNVs and indels FASTQ, BAM, VCF
Oncomine (OCA) v2/3 Thermo Fisher SNVs, indels, CNVs, fusions BAM, VCF, BAI
Ion AmpliSeq™ Cancer HotSpot Thermo Fisher SNVs and indels BAM, VCF, BAI
Hybridization
Capture
Agilent probes Agilent SNVs, indels, fusions FASTQ, BAM, VCV
Agilent/IDT probes Agilent/IDT SNVs, indels, fusions FASTQ, BAM, VCF
TruSight Tumor 170 Illumina SNVs, indels, CNVs, fusions BAM, VCFs, CSV
TruSight Cancer Illumina SNVs and indels FASTQ, BAM, VCF
Ion AmpliSeq™ Inherited Cancer Thermo Fisher SNVs and indels VCF, BAM, BAI
Haloplex
Molecular
barcodes/UMIs Agilent Haloplex Technology Agilent SNVs and indels FASTQ, BAM, VCF
Somatic Fusions
FusionPlex ALK/RET/ROS Archer Fusions FASTQ, BAM
TruSight RNA fusion Illumina Fusions FASTQ, BAM, VCF
Whole Exome
Clinical Exome
Agilent SureSelect Agilent SNVs and indels FASTQ, BAM
TruSight One Illumina SNVs and indels FASTQ, BAM, VCF
17. 17 | April 24, 2018www.pieriandx.com
REF Call
Filtering
Splice Variant
Filter
Re-
Classification
Sequence
Alignment
Variant
Identification
CNV
Conversion
Fusion
Identification
VCF Tag
Display
Primary
Variant Filter
Panel Filters
Medical
Interpretation
Therapies
Clinical Trials
Auto
Classification
Case
Accessioning
CGW Pipeline
CGW Panel
Interpretation Services
Review
Patient Data
Run QC
DNA Only RNA Only DNA/RNA
Lung
Subpanel
GIST
Subpanel
CNS
Subpanel
Colorectal
Subpanel
Melanoma
Subpanel
All Genes
Review Case
Data
DNA QC
Report
Fastq
DNA
BAM
RNA
BAM
DNA/RNA
BAM
Raw
Variant
Calls
Final
VCF
RNA QC
Report
Draft
Report
Final
Report
Data
Generation
Procedure
Selection
Auto
Interpretation
Variant QC
HGVS
Annotation
PierianDx + Illumina
TST 170 Workflow
18. 18 | April 24, 2018www.pieriandx.com
REF Call
Filtering
Splice Variant
Filter
Re-
Classification
Sequence
Alignment
Variant
Identification
CNV
Conversion
Fusion
Identification
VCF Tag
Display
Primary
Variant Filter
Panel Filters
Medical
Interpretation
Therapies
Clinical Trials
Auto
Classification
Case
Accessioning
CGW Pipeline
CGW Panel
Interpretation Services
Review
Patient Data
Run QC
DNA Only RNA Only DNA/RNA
Lung
Subpanel
GIST
Subpanel
CNS
Subpanel
Colorectal
Subpanel
Melanoma
Subpanel
All Genes
Review Case
Data
DNA QC
Report
Fastq
DNA
BAM
RNA
BAM
DNA/RNA
BAM
Raw
Variant
Calls
Final
VCF
RNA QC
Report
Draft
Report
Final
Report
Data
Generation
Procedure
Selection
Auto
Interpretation
Variant QC
HGVS
Annotation
PierianDx + Illumina
TST 170 Workflow
19. 19 | April 24, 2018www.pieriandx.com
REF Call
Filtering
Splice Variant
Filter
Re-
Classification
Sequence
Alignment
Variant
Identification
CNV
Conversion
Fusion
Identification
VCF Tag
Display
Primary
Variant Filter
Panel Filters
Medical
Interpretation
Therapies
Clinical Trials
Auto
Classification
Case
Accessioning
CGW Pipeline
CGW Panel
Interpretation Services
Review
Patient Data
Run QC
DNA Only RNA Only DNA/RNA
Lung
Subpanel
GIST
Subpanel
CNS
Subpanel
Colorectal
Subpanel
Melanoma
Subpanel
All Genes
Review Case
Data
DNA QC
Report
Fastq
DNA
BAM
RNA
BAM
DNA/RNA
BAM
Raw
Variant
Calls
Final
VCF
RNA QC
Report
Draft
Report
Final
Report
Data
Generation
Procedure
Selection
Auto
Interpretation
Variant QC
HGVS
Annotation
PierianDx + Illumina
TST 170 Workflow
20. 20 | April 24, 2018www.pieriandx.com
REF Call
Filtering
Splice Variant
Filter
Re-
Classification
Sequence
Alignment
Variant
Identification
CNV
Conversion
Fusion
Identification
VCF Tag
Display
Primary
Variant Filter
Panel Filters
Medical
Interpretation
Therapies
Clinical Trials
Auto
Classification
Case
Accessioning
CGW Pipeline
CGW Panel
Interpretation Services
Review
Patient Data
Run QC
DNA Only RNA Only DNA/RNA
Lung
Subpanel
GIST
Subpanel
CNS
Subpanel
Colorectal
Subpanel
Melanoma
Subpanel
All Genes
Review Case
Data
DNA QC
Report
Fastq
DNA
BAM
RNA
BAM
DNA/RNA
BAM
Raw
Variant
Calls
Final
VCF
RNA QC
Report
Draft
Report
Final
Report
Data
Generation
Procedure
Selection
Auto
Interpretation
Variant QC
HGVS
Annotation
CGW Pipeline
PierianDx + Illumina
TST 170 Workflow
21. 21 | April 24, 2018www.pieriandx.com
CGW Pipeline
REF Call
Filtering
Splice Variant
Filter
Re-
Classification
Sequence
Alignment
Variant
Identification
CNV
Conversion
Fusion
Identification
VCF Tag
Display
Primary
Variant Filter
Panel Filters
Medical
Interpretation
Therapies
Clinical Trials
Auto
Classification
Case
Accessioning
CGW Pipeline
CGW Panel
Interpretation Services
Review
Patient Data
Run QC
DNA Only RNA Only DNA/RNA
Lung
Subpanel
GIST
Subpanel
CNS
Subpanel
Colorectal
Subpanel
Melanoma
Subpanel
All Genes
Review Case
Data
DNA QC
Report
Fastq
DNA
BAM
RNA
BAM
DNA/RNA
BAM
Raw
Variant
Calls
Final
VCF
RNA QC
Report
Draft
Report
Final
Report
Data
Generation
Procedure
Selection
Auto
Interpretation
Variant QC
HGVS
Annotation
PierianDx + Illumina
TST 170 Workflow
22. 22 | April 24, 2018www.pieriandx.com
CGW Pipeline
REF Call
Filtering
Splice Variant
Filter
Re-
Classification
Sequence
Alignment
Variant
Identification
CNV
Conversion
Fusion
Identification
VCF Tag
Display
Primary
Variant Filter
Panel Filters
Medical
Interpretation
Therapies
Clinical Trials
Auto
Classification
Case
Accessioning
CGW Pipeline
CGW Panel
Interpretation Services
Review
Patient Data
Run QC
DNA Only RNA Only DNA/RNA
Lung
Subpanel
GIST
Subpanel
CNS
Subpanel
Colorectal
Subpanel
Melanoma
Subpanel
All Genes
Review Case
Data
DNA QC
Report
Fastq
DNA
BAM
RNA
BAM
DNA/RNA
BAM
Raw
Variant
Calls
Final
VCF
RNA QC
Report
Draft
Report
Final
Report
Data
Generation
Procedure
Selection
Auto
Interpretation
Variant QC
HGVS
Annotation
PierianDx + Illumina
TST 170 Workflow
23. 23 | April 24, 2018www.pieriandx.com
Interpretation Services
The PierianDx Advantage
Collaboration
Consider our team an extension
of your team.
The SOP we follow is developed in
collaboration with our clients for our
clients to meet their unique needs.
Clinical Content
100% clinically curated content
(vs. research)
Use our written interpretations and all
our clinical content to sign-out cases
more efficiently now and in the future.
Our Team is Your Team
30+ variant analysts with medical + scientific
expertise. Includes PhDs and MDs trained at
Johns Hopkins, MD Anderson, Tufts University,
University of Pittsburgh, University of Texas,
Penn State University, and Sanford-Burnham.
Communication
Have a question or need to relay extra
info about a complex case?
Enjoy direct access to our interpretive
services director and medical director*
as needed. Available for Tumor Board.
* Medical Director Review and Medical Director Signout
available within Tier II and Tier III service levels.
Integrated Workflow
24. 24 | April 24, 2018www.pieriandx.com
Planning, Assay Selection
Foundation for Success
Planning
■ Initial Consultation
■ Assess feasibility of business plan
■ Share best practices
■ Design implementation roadmap
■ Planning
■ Meetings with clinical leadership
■ Develop quarterly assay portfolio
■ Share best practices and planning
■ Operational Preparation
■ Establish method development
■ Provide CLIA and CAP assistance
■ Lab workflow for NGS testing.
Assay Selection
■ Turnkey Panel Assessment
■ Cancer Type Selection
■ Panel Assessment
■ Assay Recommendation
■ Custom Assay Design
■ Cancer Type Selection
■ Evidence based Panel Design
■ Target Gene List
■ Order Custom Panel Design with
Reagent Vendor
Planning
■ Initial Consultation
■ Assess feasibility of business plan
■ Share best practices
■ Design implementation roadmap
■ Planning
■ Meetings with clinical leadership
■ Develop quarterly assay portfolio
■ Share best practices and planning
■ Operational Preparation
■ Establish method development
■ Provide CLIA and CAP assistance
■ Lab workflow for NGS testing.
25. 25 | April 24, 2018www.pieriandx.com
Trusted Assay Validation Services
Accelerate Your Go-Live
NGS Assay
Validation Support
Development of draft validation plan
Assay familiarization and optimization
Validation analyses and data review
Analytical sensitivity and specificity
Precision concordance, reproducibility
QC references, exon/hotspot coverage
Sample procurement
✓
✓
✓
✓
✓
✓
✓
✓
✓
Case Study: Moffit STAR
1st Clinically Validated and Live TST 170 Assay
PierianDx was instrumental in Moffitt’s validation and
implementation of TST170. We continue to work with
Moffitt and other Sequoia group members to optimize
workflows and validate TMB and MSI.
Report, requisition & consent forms
CAP/CLIA compliant documentation
26. 26 | April 24, 2018www.pieriandx.com
Physician Engagement
Education & Awareness
NGS Fast Forward Program
■ Fast Forward Program Guide
■ Physician Outreach Tools
■ Assay Spec Sheet
■ Sample Report
■ Assist with Requisition Form
■ Available Insight Papers
■ Participation in Physician Kick-off Meeting
■ Molecular Tumor Board Participation
■ Onsite Grand Rounds by PierianDx
Medical Director
27. 27 | April 24, 2018www.pieriandx.com
Actionable
Intelligence
28. 28 | April 24, 2018www.pieriandx.com
Cloud-Based
Technology Integration
API, HL7 - order entry LDAP
- certificate for
authentication systems
Automated NGS
data transfer
API - Discrete data to
Decision Support App, EDW
API, HL7 -
PDF report transfer
to EMR
Hospital Lab
API - Discrete
data to
3rd party apps
29. 29 | April 24, 2018www.pieriandx.com
Actionable Intelligence
Drug Disease
Drug Class
Knowledge Source
Management Impact
Drug Impact
Prognostic Impact
Clinical Trials in US
KnowledgeSpace
■ ASCO, NCCN guidelines
■ Public sources
■ Curated knowledge sources
■ FDA therapies, clinical trials
■ Published literature
■ Medical interpretations from
PierianDx
and shared by
customers.
Machine learning.
Human acumen.
Collaborative network.
29 | April 20, 2018www.pieriandx.com
30. 30 | April 24, 2018www.pieriandx.com
Cumulative Patient Care Case Volume
KnowledgeSpace Growth
Production Stats
150+ Unique NGS Panels
80+ Molecular Pathologists
1,130+ Diseases tested
1,080+ Somatic genes
32. 32 | April 24, 2018www.pieriandx.com
Webinar
cs
1
3
4
Positive Industry Trends
with Challenges
Actionable Intelligence Delivers
Value to the Enterprise
Complete Clinical Genomics
Solutions are Required
2
Your Peers are Innovating with
Precision Medicine
Summary
Topics Covered
32 | April 24, 2018
33. 33 | April 24, 2018www.pieriandx.com
cs
Our Business is Your Business
How May We Assist?
Schedule a
free consultation with a
clinical genomics expert
Accelerate your assay validation
Improve the quality of your genomic reports
Optimize your clinical workflow
Increase your genomic testing volume
34. 34 | April 24, 2018www.pieriandx.com
Thank You
Q&A
BG Jones
SVP, Business Development
BGJones@PierianDx.com
Editor's Notes
Learn how to develop the right approach to planning and implementing molecular testing in your lab.
Be introduced the spectrum of PierianDx services that complement our technology, including: precision medicine planning, assay selection, physician engagement, validation, technology integration, interpretation and lab services.
Understand the benefits of PierianDx's Actionable Intelligence engine, a constantly learning knowledgebase of millions of biomedical findings.
Discover real-world examples of how academic medical centers, health systems, and cancer centers have implemented best practices to expand their programs and improve outcomes for patients.
Need help? Check out our Building a Backable Team module and weekly strategy session.